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- PDB-7b3o: Crystal structure of the SARS-CoV-2 RBD in complex with STE90-C11 Fab -

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Basic information

Entry
Database: PDB / ID: 7b3o
TitleCrystal structure of the SARS-CoV-2 RBD in complex with STE90-C11 Fab
Components
  • Heavy Chain of Fab Fragment
  • Light Chain of Fab Fragment
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / neutralizing antibodies / SARS-CoV-2 / RBD
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKluenemann, T. / Van den Heuvel, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
Citation
Journal: Cell Rep / Year: 2021
Title: A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations.
Authors: Bertoglio, F. / Fuhner, V. / Ruschig, M. / Heine, P.A. / Abassi, L. / Klunemann, T. / Rand, U. / Meier, D. / Langreder, N. / Steinke, S. / Ballmann, R. / Schneider, K.T. / Roth, K.D.R. / ...Authors: Bertoglio, F. / Fuhner, V. / Ruschig, M. / Heine, P.A. / Abassi, L. / Klunemann, T. / Rand, U. / Meier, D. / Langreder, N. / Steinke, S. / Ballmann, R. / Schneider, K.T. / Roth, K.D.R. / Kuhn, P. / Riese, P. / Schackermann, D. / Korn, J. / Koch, A. / Chaudhry, M.Z. / Eschke, K. / Kim, Y. / Zock-Emmenthal, S. / Becker, M. / Scholz, M. / Moreira, G.M.S.G. / Wenzel, E.V. / Russo, G. / Garritsen, H.S.P. / Casu, S. / Gerstner, A. / Roth, G. / Adler, J. / Trimpert, J. / Hermann, A. / Schirrmann, T. / Dubel, S. / Frenzel, A. / Van den Heuvel, J. / Cicin-Sain, L. / Schubert, M. / Hust, M.
#1: Journal: Cell Rep / Year: 2021
Title: A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations.
Authors: Bertoglio, F. / Fuhner, V. / Ruschig, M. / Heine, P.A. / Abassi, L. / Klunemann, T. / Rand, U. / Meier, D. / Langreder, N. / Steinke, S. / Ballmann, R. / Schneider, K.T. / Roth, K.D.R. / ...Authors: Bertoglio, F. / Fuhner, V. / Ruschig, M. / Heine, P.A. / Abassi, L. / Klunemann, T. / Rand, U. / Meier, D. / Langreder, N. / Steinke, S. / Ballmann, R. / Schneider, K.T. / Roth, K.D.R. / Kuhn, P. / Riese, P. / Schackermann, D. / Korn, J. / Koch, A. / Chaudhry, M.Z. / Eschke, K. / Kim, Y. / Zock-Emmenthal, S. / Becker, M. / Scholz, M. / Moreira, G.M.S.G. / Wenzel, E.V. / Russo, G. / Garritsen, H.S.P. / Casu, S. / Gerstner, A. / Roth, G. / Adler, J. / Trimpert, J. / Hermann, A. / Schirrmann, T. / Dubel, S. / Frenzel, A. / Van den Heuvel, J. / Cicin-Sain, L. / Schubert, M. / Hust, M.
#2: Journal: Biorxiv / Year: 2020
Title: A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients by phage display is binding to the ACE2-RBD interface and is tolerant to known RBD mutations
Authors: Bertoglio, F. / Fuhner, V. / Ruschig, M. / Heine, P.A. / Rand, U. / Klunemann, T. / Meier, D. / Langreder, N. / Steinke, S. / Ballmann, R. / Schneider, K. / Roth, K.D.R. / Kuhn, P. / Riese, ...Authors: Bertoglio, F. / Fuhner, V. / Ruschig, M. / Heine, P.A. / Rand, U. / Klunemann, T. / Meier, D. / Langreder, N. / Steinke, S. / Ballmann, R. / Schneider, K. / Roth, K.D.R. / Kuhn, P. / Riese, P. / Schackermann, D. / Korn, J. / Koch, A. / Zock-Emmenthal, S. / Becker, M. / Scholz, M. / Moreira, G.M.S.G. / Wenzel, E.V. / Russo, G. / Garritsen, H.S. / Casu, S. / Gerstner, A. / Roth, G. / Hermann, A. / Schirrmann, T. / Dubel, S. / Frenzel, A. / Cicin-Sain, L. / Schubert, M. / Hust, M.
History
DepositionDec 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Aug 4, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
L: Light Chain of Fab Fragment
H: Heavy Chain of Fab Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0754
Polymers70,6513
Non-polymers4241
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-21 kcal/mol
Surface area27040 Å2
Unit cell
Length a, b, c (Å)195.756, 87.420, 57.059
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-435-

HOH

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Components

#1: Protein Spike protein S1


Mass: 23087.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody Light Chain of Fab Fragment


Mass: 23481.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Heavy Chain of Fab Fragment


Mass: 24081.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 13.3% (w/v) polyethylene glycol 6,000, 0.1M MES pH 5.6 0.24M tri sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→48.1 Å / Num. obs: 63906 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Net I/σ(I): 6.7 / Num. measured all: 437879 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.71.8943020745010.6530.7872.0541.2100
9.17-48.17.20.09650507060.9790.0410.10517.399.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å48.09 Å
Translation2 Å48.09 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7bwy

7bwy


Resolution: 2→48.1 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 1088 1.7 %
Rwork0.1852 62762 -
obs0.1859 63850 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.82 Å2 / Biso mean: 47.2921 Å2 / Biso min: 22.59 Å2
Refinement stepCycle: final / Resolution: 2→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 53 427 5147
Biso mean--113.03 43.17 -
Num. residues----613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.090.36381350.319178037938
2.09-2.20.33161360.272978067942
2.2-2.340.27451350.238977637898
2.34-2.520.26451360.221978417977
2.52-2.770.26121350.219478207955
2.77-3.170.21251360.195978818017
3.17-40.21781370.163978688005
4-48.10.1751380.139879808118

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